Abstract

The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order to study the molecular interactions in atomistic molecular dynamics (MD) simulations. The multiscale coarse-graining (MS-CG) approach enables the computation of the many-body PMF of an atomistic system in terms of the CG coordinates, which can be used to parameterize CG models based on all-atom configurations. We demonstrate here that the MS-CG method can also be used to analyze the CG interactions from atomistic MD trajectories via PMF calculations. In addition, MS-CG calculations at different temperatures are performed to decompose the PMF values into energetic and entropic contributions as a function of the CG coordinates, which provides more thermodynamic information regarding the atomistic system. Two numerical examples, liquid methanol and a dimyristoylphosphatidylcholine lipid bilayer, are presented. The results show that MS-CG can be used as an analysis tool, comparable to various free energy computation methods. The differences between the MS-CG approach and other PMF calculation methods, as well as the characteristics and advantages of MS-CG, are also discussed.

Received 27 February 2011Accepted 20 May 2011Published online 14 June 2011

Acknowledgments:

This research was supported by a National Science Foundation Collaborative Research in Chemistry Grant (CHE-0628257 and CHE-1047323). Computer resources were provided by the National Science Foundation (NSF) through TeraGrid computing resources administered by the Pittsburgh Supercomputing Center, the San Diego Supercomputer Center, the National Center for Supercomputing Applications, the Texas Advanced Computing Center, and Argonne National Laboratory. We thank Dr. Ryan Jorn for a critical reading of the manuscript and insightful discussions.